FMO DATABASE

FMODB ID: JL479

Calculation Name: 5VXB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VXB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ABV9

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1652874.513173
FMO2-HF: Nuclear repulsion	1589087.57354
FMO2-HF: Total energy	-63786.939632
FMO2-MP2: Total energy	-63973.148617

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-3.523	1.779	8.505	-3.988	-9.818	-0.028

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.019

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	THR	0	-0.033	-0.019	3.490	-2.316	-0.806	0.002	-0.824	-0.689	0.001
4	A	4	ARG	1	0.858	0.887	6.146	1.026	1.026	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.002	0.004	9.116	0.209	0.209	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.778	-0.894	6.750	-0.342	-0.342	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.031	-0.003	8.508	0.293	0.293	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.032	-0.022	9.741	0.026	0.026	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.043	0.025	12.017	0.025	0.025	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.009	-0.002	10.136	0.074	0.074	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.000	-0.015	12.231	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.838	-0.896	14.797	0.256	0.256	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.047	-0.017	14.981	-0.030	-0.030	0.000	0.000	0.000	0.000
14	A	14	HIS	0	-0.051	-0.027	13.389	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.007	0.006	17.805	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.063	-0.012	15.789	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.798	-0.868	18.450	0.222	0.222	0.000	0.000	0.000	0.000
18	A	18	HIS	1	0.849	0.894	16.879	-0.207	-0.207	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.895	0.951	19.402	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.033	-0.037	15.730	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.003	0.000	18.509	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.801	-0.872	16.578	-0.237	-0.237	0.000	0.000	0.000	0.000
23	A	23	HIS	0	-0.033	-0.010	17.845	0.045	0.045	0.000	0.000	0.000	0.000
24	A	24	PRO	0	0.046	0.010	18.667	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.018	0.008	16.350	0.023	0.023	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.003	0.014	18.670	0.012	0.012	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.017	-0.015	18.547	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.731	0.828	23.173	0.120	0.120	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.017	0.007	26.410	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.811	-0.899	28.821	-0.086	-0.086	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.771	-0.871	25.230	-0.118	-0.118	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.002	0.000	24.962	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.045	-0.017	25.992	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.882	-0.941	27.287	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.019	-0.009	21.651	0.008	0.008	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.891	0.938	24.529	0.040	0.040	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.011	0.007	26.486	0.012	0.012	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.010	0.003	25.487	0.009	0.009	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.113	-0.036	20.098	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.090	0.055	24.832	0.001	0.001	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.043	0.028	25.209	0.010	0.010	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.015	0.005	24.329	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.029	-0.030	21.691	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.009	-0.026	17.884	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.773	0.899	18.650	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.003	0.006	14.448	0.080	0.080	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.000	-0.002	15.775	-0.054	-0.054	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.067	0.045	9.932	0.045	0.045	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.045	-0.023	14.228	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.930	0.950	14.472	0.227	0.227	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.735	-0.862	16.795	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.040	-0.028	19.965	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.847	0.923	21.164	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.002	0.015	18.246	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.050	-0.013	14.032	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.014	-0.004	9.959	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	57	TRP	0	-0.002	-0.017	13.641	0.070	0.070	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.010	-0.001	11.451	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.007	0.009	14.578	0.040	0.040	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.015	-0.006	16.424	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.010	-0.026	18.653	0.011	0.011	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.030	0.019	21.373	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.012	0.000	23.207	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.883	-0.948	24.026	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.043	-0.024	25.534	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.015	0.003	26.144	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.033	0.006	22.370	0.009	0.009	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.803	-0.899	26.465	-0.039	-0.039	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.013	-0.010	21.800	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.823	0.902	24.941	0.078	0.078	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.935	0.972	28.037	0.021	0.021	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.057	0.028	22.863	0.003	0.003	0.000	0.000	0.000	0.000
73	A	73	HIS	0	0.033	0.029	24.747	0.001	0.001	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.056	-0.034	25.706	0.008	0.008	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.002	0.029	26.825	0.004	0.004	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.022	-0.002	20.744	0.009	0.009	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.027	0.025	23.378	0.011	0.011	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.003	0.004	21.241	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.061	-0.030	22.040	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.874	0.920	23.603	0.048	0.048	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.049	0.033	19.996	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.044	-0.024	20.430	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.053	0.020	17.732	0.009	0.009	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.008	0.009	14.295	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.020	-0.010	13.270	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.027	-0.012	10.998	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.845	-0.913	9.459	-0.810	-0.810	0.000	0.000	0.000	0.000
88	A	88	MET	0	0.027	0.011	8.584	-0.208	-0.208	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.031	0.013	7.704	-0.058	-0.058	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.017	0.008	3.760	-0.030	0.161	0.000	-0.026	-0.165	0.000
91	A	91	GLU	-1	-0.863	-0.921	4.038	-2.270	-1.941	0.000	-0.061	-0.267	0.000
92	A	92	THR	0	-0.071	-0.055	3.754	-1.009	-0.628	0.009	-0.121	-0.269	-0.001
93	A	93	LEU	0	0.008	0.000	4.732	0.629	0.734	-0.001	-0.006	-0.098	0.000
94	A	94	GLY	0	0.003	0.015	2.481	0.848	1.294	2.155	-1.486	-1.116	0.006
95	A	95	VAL	0	-0.042	-0.012	3.093	-2.571	-3.012	0.049	1.159	-0.767	-0.005
96	A	96	THR	0	0.025	0.009	5.924	-0.035	-0.035	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.042	-0.008	9.068	0.155	0.155	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.017	-0.001	12.577	-0.049	-0.049	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.010	0.019	9.670	0.036	0.036	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.011	0.003	10.286	0.054	0.054	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.026	-0.032	9.386	0.044	0.044	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.069	0.042	10.927	0.107	0.107	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.000	-0.015	10.338	0.149	0.149	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.050	0.021	6.942	0.304	0.304	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.004	-0.004	6.313	0.725	0.725	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.003	0.018	4.829	0.111	0.111	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.025	-0.032	2.255	2.705	3.992	5.016	-2.046	-4.256	-0.015
108	A	108	ASP	-1	-0.767	-0.870	2.687	-1.750	-0.881	1.243	-0.424	-1.688	-0.014
109	A	109	THR	0	-0.088	-0.089	4.099	-0.276	0.288	0.033	-0.149	-0.449	0.000
110	A	110	GLU	-1	-0.894	-0.919	5.092	0.478	0.478	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.819	0.923	7.516	-1.614	-1.614	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.824	0.897	5.281	1.097	1.097	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.066	-0.040	8.334	-0.102	-0.102	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.951	0.984	11.050	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	115	PHE	0	0.047	0.015	13.885	-0.038	-0.038	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.027	-0.016	15.444	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.015	-0.006	18.799	0.003	0.003	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.741	-0.859	21.067	0.059	0.059	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.871	0.916	24.359	-0.101	-0.101	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.043	0.020	27.286	0.005	0.005	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.044	-0.007	19.978	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.020	-0.017	24.004	0.017	0.017	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.808	-0.877	24.965	0.133	0.133	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.052	-0.022	25.415	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.810	-0.903	25.750	0.184	0.184	0.000	0.000	0.000	0.000
126	A	126	PRO	0	-0.031	-0.001	23.325	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.041	-0.027	20.039	-0.016	-0.016	0.000	0.000	0.000	0.000
128	A	128	ASN	0	-0.009	-0.017	18.998	0.013	0.013	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.018	0.016	14.346	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	HIS	0	0.018	0.013	12.033	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	131	PRO	0	-0.021	0.013	11.064	0.113	0.113	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.031	-0.029	4.436	-0.180	-0.119	-0.001	-0.004	-0.054	0.000
133	A	133	LYS	1	0.855	0.906	7.579	0.459	0.459	0.000	0.000	0.000	0.000
134	A	134	ASN	0	0.010	-0.011	10.096	0.069	0.069	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.835	-0.896	13.125	-0.513	-0.513	0.000	0.000	0.000	0.000
136	A	136	ALA	0	0.022	0.015	14.052	0.028	0.028	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.002	-0.014	15.042	0.004	0.004	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.058	-0.033	15.088	-0.009	-0.009	0.000	0.000	0.000	0.000
139	A	139	ALA	0	0.041	0.041	17.073	0.025	0.025	0.000	0.000	0.000	0.000
140	A	140	VAL	0	-0.006	-0.009	16.954	0.013	0.013	0.000	0.000	0.000	0.000
141	A	141	SER	0	0.017	-0.009	20.226	-0.011	-0.011	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.011	-0.006	21.577	0.062	0.062	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.004	-0.010	22.229	0.030	0.030	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.042	0.018	20.414	0.034	0.034	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.006	0.000	16.432	0.068	0.068	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.816	0.890	17.753	-0.184	-0.184	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.869	0.918	19.080	-0.271	-0.271	0.000	0.000	0.000	0.000
148	A	148	PHE	0	0.005	0.004	9.945	0.057	0.057	0.000	0.000	0.000	0.000
149	A	149	LEU	0	-0.018	-0.013	14.154	0.129	0.129	0.000	0.000	0.000	0.000
150	A	150	ALA	0	0.005	0.005	15.547	0.053	0.053	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.004	0.004	14.540	0.022	0.022	0.000	0.000	0.000	0.000
152	A	152	LEU	0	-0.047	-0.011	9.248	0.200	0.200	0.000	0.000	0.000	0.000
153	A	153	GLY	0	-0.001	0.011	12.249	0.066	0.066	0.000	0.000	0.000	0.000
154	A	154	VAL	0	-0.066	-0.039	11.917	-0.055	-0.055	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.905	-0.953	15.099	0.299	0.299	0.000	0.000	0.000	0.000
156	A	156	PRO	0	-0.073	-0.027	18.288	-0.018	-0.018	0.000	0.000	0.000	0.000
157	A	157	MET	0	-0.002	0.001	19.208	-0.034	-0.034	0.000	0.000	0.000	0.000
158	A	158	ILE	0	0.005	0.001	21.427	-0.013	-0.013	0.000	0.000	0.000	0.000
159	A	159	VAL	0	-0.013	-0.009	23.741	-0.012	-0.012	0.000	0.000	0.000	0.000
160	A	160	ASP	-1	-0.812	-0.893	25.960	0.059	0.059	0.000	0.000	0.000	0.000
161	A	161	PHE	0	0.000	-0.032	22.936	-0.009	-0.009	0.000	0.000	0.000	0.000
162	A	162	ALA	0	-0.051	-0.011	28.954	-0.010	-0.010	0.000	0.000	0.000	0.000
163	A	163	ALA	0	0.003	0.002	32.690	-0.006	-0.006	0.000	0.000	0.000	0.000
164	A	164	MET	0	-0.117	-0.053	28.228	-0.004	-0.004	0.000	0.000	0.000	0.000
165	A	165	GLU	-1	-0.901	-0.947	30.353	0.055	0.055	0.000	0.000	0.000	0.000
166	A	166	VAL	0	-0.030	-0.023	25.645	0.006	0.006	0.000	0.000	0.000	0.000
167	A	167	VAL	0	-0.031	-0.012	27.522	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)